Variant report

Variant	rs9894807
Chromosome Location	chr17:38330178-38330179
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYBL2	chr17:38329435-38330269	HepG2	liver:	n/a	n/a
2	POLR2A	chr17:38329380-38330432	Hela-S3	cervix:	n/a	n/a
3	SP1	chr17:38329587-38330201	HepG2	liver:	n/a	n/a
4	POLR2A	chr17:38330123-38330395	GM12892	blood:	n/a	n/a
5	POLR2A	chr17:38330099-38330438	K562	blood:	n/a	n/a
6	POLR2A	chr17:38329354-38330335	HepG2	liver:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:38330143-38330193	HIPEpiC	eye:	n/a
2	chr17:38330143-38330193	HUVEC	blood vessel:	n/a
3	chr17:38330143-38330193	NHDF-neo	bronchial:	n/a
4	chr17:38330143-38330193	CMK	blood:	n/a
5	chr17:38330143-38330193	AG04449	skin:	fetal
6	chr17:38330143-38330193	LNCaP	prostate:	n/a
7	chr17:38330143-38330193	NHBE	bronchial:	n/a
8	chr17:38330143-38330193	HAEpiC	amniotic membrane:	n/a
9	chr17:38330143-38330193	HEK293	kidney:	embryo
10	chr17:38330143-38330193	U87	brain:	n/a
11	chr17:38330143-38330193	AoSMC	blood vessel:	n/a
12	chr17:38330143-38330193	HNPCEpiC	eye:	n/a
13	chr17:38330143-38330193	BE2_C	brain:	n/a
14	chr17:38330143-38330193	NT2-D1	testis:	n/a
15	chr17:38330143-38330193	HPAEpiC	pulmonary alveolar:	n/a
16	chr17:38330143-38330193	SAEC	small airway:	n/a
17	chr17:38330143-38330193	ovcar-3	ovarian:	n/a
18	chr17:38330143-38330193	BJ	skin:	n/a
19	chr17:38330143-38330193	A549	lung:	n/a
20	chr17:38330143-38330193	RPTEC	kidney:	n/a
21	chr17:38330143-38330193	HCM	heart:	n/a
22	chr17:38330143-38330193	Caco-2	colon:	n/a
23	chr17:38330143-38330193	GM19239	blood:	n/a
24	chr17:38330143-38330193	ProgFib	skin:	n/a
25	chr17:38330143-38330193	SK-N-SH_RA	brain:	n/a
26	chr17:38330143-38330193	MCF10A-Er-Src	breast:	n/a
27	chr17:38330143-38330193	AG04450	lung:	fetal
28	chr17:38330143-38330193	HepG2	liver:	n/a
29	chr17:38330143-38330193	T-47D	breast:	n/a
30	chr17:38330143-38330193	GM12891	blood:	n/a
31	chr17:38330143-38330193	HRE	kidney:	n/a
32	chr17:38330143-38330193	IMR90	lung:	fetal
33	chr17:38330143-38330193	Jurkat	blood:	n/a
34	chr17:38330143-38330193	HRPEpiC	eye:	n/a
35	chr17:38330143-38330193	HRCEpiC	kidney:	n/a
36	chr17:38330143-38330193	HCPEpiC	choroid plexus:	n/a
37	chr17:38330143-38330193	H1-hESC	embryonic stem cell:	embryo
38	chr17:38330143-38330193	NB4	blood:	n/a
39	chr17:38330143-38330193	Hepatocyte	liver:	n/a
40	chr17:38330143-38330193	Hela-S3	cervix:	n/a
41	chr17:38330143-38330193	K562	blood:	n/a
42	chr17:38330143-38330193	PFSK-1	brain:	n/a
43	chr17:38330143-38330193	HEEpiC	esophagus:	n/a
44	chr17:38330143-38330193	AG09319	gingival:	n/a
45	chr17:38330143-38330193	SKMC	muscle:	n/a
46	chr17:38330143-38330193	GM06990	blood:	n/a
47	chr17:38330143-38330193	ECC-1	luminal epithelium:	n/a
48	chr17:38330143-38330193	SK-N-MC	brain:	n/a
49	chr17:38330143-38330193	MCF-7	breast:	n/a
50	chr17:38330143-38330193	HMEC	breast:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38330070..38334400-chr17:38346938..38351108,4	K562	blood:
2	chr17:38296837..38298632-chr17:38328286..38330912,2	K562	blood:
3	chr17:38324296..38327279-chr17:38328642..38330964,3	K562	blood:
4	chr17:38327969..38330212-chr17:38330678..38333544,4	K562	blood:

No data

Variant related genes	Relation type
RAPGEFL1	TF binding region
RAPGEFL1	CpG island
ENSG00000108349	Chromatin interaction
ENSG00000108352	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10512482	1.00[CEU][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1104761	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11540720	0.85[EUR][1000 genomes]
rs12103533	1.00[CEU][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs15685	0.92[EUR][1000 genomes]
rs16965660	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs16965669	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16965734	0.85[EUR][1000 genomes]
rs16965736	0.85[EUR][1000 genomes]
rs16965748	0.85[EUR][1000 genomes]
rs16965774	0.85[EUR][1000 genomes]
rs16965778	0.85[EUR][1000 genomes]
rs17616543	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17616672	0.92[EUR][1000 genomes]
rs17616879	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17617263	0.92[EUR][1000 genomes]
rs17678817	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17678959	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17678990	0.92[EUR][1000 genomes]
rs17679086	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17679361	0.92[EUR][1000 genomes]
rs17680217	0.92[EUR][1000 genomes]
rs17680410	0.92[EUR][1000 genomes]
rs17680507	0.92[EUR][1000 genomes]
rs17680624	0.92[EUR][1000 genomes]
rs2012667	0.92[EUR][1000 genomes]
rs2229773	0.92[EUR][1000 genomes]
rs28362320	0.85[EUR][1000 genomes]
rs28362321	0.92[EUR][1000 genomes]
rs28526298	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs33998939	0.92[EUR][1000 genomes]
rs34270904	0.85[EUR][1000 genomes]
rs34300454	0.85[EUR][1000 genomes]
rs35783632	0.92[EUR][1000 genomes]
rs35898909	0.92[EUR][1000 genomes]
rs41283417	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs41283423	0.92[EUR][1000 genomes]
rs4134993	0.92[EUR][1000 genomes]
rs4134998	0.92[EUR][1000 genomes]
rs4135005	0.92[EUR][1000 genomes]
rs4135007	0.92[EUR][1000 genomes]
rs4135012	0.92[EUR][1000 genomes]
rs4135019	0.92[EUR][1000 genomes]
rs4135021	0.92[EUR][1000 genomes]
rs4135027	0.92[EUR][1000 genomes]
rs4135030	0.92[EUR][1000 genomes]
rs45612441	0.92[EUR][1000 genomes]
rs8067519	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8071687	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8077482	0.85[EUR][1000 genomes]
rs9889905	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9891944	0.92[EUR][1000 genomes]
rs9894364	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9898500	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9899425	0.85[EUR][1000 genomes]
rs9900154	1.00[CEU][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9903293	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9906274	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9909777	1.00[CEU][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9909811	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9910373	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9915775	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833444	chr17:38242823-38437280	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv525796	chr17:38306365-38405037	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38297800-38333000	Strong transcription	Fetal Muscle Trunk	muscle
2	chr17:38297800-38336600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr17:38298000-38330400	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr17:38298000-38330800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr17:38298200-38333000	Strong transcription	Fetal Thymus	thymus
6	chr17:38298600-38332200	Strong transcription	Fetal Intestine Small	intestine
7	chr17:38308200-38333200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr17:38314200-38333000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr17:38314800-38333200	Weak transcription	Right Atrium	heart
10	chr17:38315400-38331000	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr17:38315400-38331400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr17:38315600-38333000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr17:38315600-38333000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr17:38315800-38331400	Strong transcription	Fetal Intestine Large	intestine
15	chr17:38316200-38333200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr17:38316400-38331400	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr17:38317000-38333000	Strong transcription	Spleen	Spleen
18	chr17:38317200-38330600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr17:38317200-38331000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr17:38317200-38333200	Strong transcription	Thymus	Thymus
21	chr17:38317400-38330400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr17:38317400-38331200	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr17:38317400-38331400	Strong transcription	Primary B cells from peripheral blood	blood
24	chr17:38317400-38333400	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr17:38317400-38333800	Strong transcription	Dnd41	blood
26	chr17:38317600-38330400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr17:38317600-38330400	Strong transcription	Duodenum Mucosa	Duodenum
28	chr17:38317600-38333000	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr17:38317600-38333000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr17:38317600-38333200	Strong transcription	Left Ventricle	heart
31	chr17:38317800-38330200	Strong transcription	H9 Cell Line	embryonic stem cell
32	chr17:38317800-38330400	Strong transcription	GM12878-XiMat	blood
33	chr17:38317800-38330600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr17:38317800-38331400	Strong transcription	Lung	lung
35	chr17:38317800-38332800	Strong transcription	Brain Hippocampus Middle	brain
36	chr17:38318000-38331400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr17:38318000-38331400	Strong transcription	Brain Germinal Matrix	brain
38	chr17:38320600-38332800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr17:38321400-38331000	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr17:38322400-38332000	Strong transcription	Fetal Brain Female	brain
41	chr17:38322400-38333200	Weak transcription	Psoas Muscle	Psoas
42	chr17:38323800-38332800	Strong transcription	Right Ventricle	heart
43	chr17:38324600-38332400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr17:38324600-38332800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr17:38324600-38333000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr17:38324800-38330200	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr17:38324800-38330200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr17:38324800-38330400	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr17:38324800-38330400	Strong transcription	HSMM	muscle
50	chr17:38324800-38330600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links